Sensitive detection of bacteria by improved nested polymerase chain reaction targeting the 16S ribosomal RNA gene and identification of bacterial species by amplicon sequencing

ABSTRACT

A method for identifying an RNA form of a bacteria, comprising reverse transcribing RNA material; conducting PCR using primers for a first highly conserved genetic sequence generic of the bacteria; conducting nested PCR using primers for a second highly conserved genetic sequence within the first genetic sequence of the bacteria; and identifying the bacteria based on unconserved amplified sequences linked to the conserved sequences.

RELATED APPLICATIONS

The present application is a continuation of U.S. patent application Ser. No. 11/204,854, filed Aug. 15, 2005, which claims benefit of priority from U.S. Provisional Patent Application 60/603,120, filed Aug. 20, 2004, each of which is expressly incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to the field of PCR methods, and specific primers therefore, as well as their use in the identification of any type of bacteria, and in particular RNA forms of bacteria.

BACKGROUND OF THE INVENTION

The use of biological fluids for therapeutic human application such as plasmas, albumin, live vaccines, stem cells requires that they are absolutely devoid of bacterial contamination. It has been found that filtering, and possibly other traditional methods, may fail to eliminate all forms of organisms, leading to possible contamination or experimental artifacts.

It is believed that certain pathologies are associated with bacteria or bacterial forms which are difficult to detect, and which may pass through nano-porous barriers. This leads to possible errors in diagnosis or causation, and which may lead to erroneous treatment and impede prevention.

See, Hopert, Anne, Uphoff, Cord C., Wirth, Manfred, Hauser, Hansjorg, and Drexler, Hans G., “Specificity and sensitivity of Polymerase Chain Reaction (PCR) in comparison with other methods for the detection of mycoplasma contamination in cell lines”, J. Immunological Methods, 164 (1993):91-100, expressly incorporated herein by reference.

Kajander, E. O., et al., “Comparison of Staphylococci and novel Bacteria-Like Particles from blood”, Zbl. Bakt. Suppl. 26, 1994, expressly incorporated herein by reference.

Akerman, Kari K., “Scanning Electron Microscopy of Nanobacteria—Novel Biofilm Producing Organisms in Blood”, Scanning Vol. 15, Suppl. III (1993), expressly incorporated herein by reference. www.newcastle.edu.au/discipline/biology/projects/hons_cpru.html, expressly incorporated herein by reference.

Cifticioglu, Neva, et al., “Apoptotic effect of nanobacteria on cultured mammalian cells”, Mol. Biol. Cell. Suppl., Vol. 7 (1996):517a

Cifticioglu, Neva, et al., “A new potential threat in antigen and antibody products: Nanobacteria”, Vaccines 97, Brown et al. Ed., Cold Spring Harbor Laboratory Press, New York, 1997, expressly incorporated herein by reference.

Baseman, Joel B., et al., “Mycoplasmas: Sophisticated, Reemerging, and Burdened by their Notoriety”, EID Vol. 3, N^(o) 1 www.cdc.gov/ncidod/EID/vol3nol/baseman.htm, expressly incorporated herein by reference.

Relman, David A., “Detection and Identification of Previously Unrecognized Microbial Pathogens”, EID Vol. 4, N^(o) 3 www.cdc.gov/ncidod/EID/vol4no3/relman.htm, expressly incorporated herein by reference.

Mattman, Lida H., Cell Wall Deficient Forms-Stealth Pathogens, 2nd Ed., CRC Press (1993), expressly incorporated herein by reference.

U.S. Pat. No. 5,688,646, expressly incorporated herein by reference, describes novel mycoplasmas which are prominent in patients who are thought to be suffering from AIDS. Devices are also provided for the in vitro detection of mycoplasmas in biological fluid by means of a reagent which is specific for the mycoplasma group without being specific for particular species within said group. Devices for testing mycoplasma sensitivity to antibiotics are also described.

See the following, each of which and cited references is expressly incorporated herein by reference in their entirety:

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SUMMARY OF THE INVENTION

The present invention allows improved detection of such bacterial contaminants, including unconventional forms such as filtering forms (nanoforms), nanobacteria, and L-forms.

Its Principal Applications are the:

-   -   Detection of very low levels of mycoplasma contamination of cell         lines and biological fluids     -   Identification of latent bacterial infections in various         pathologies     -   Detection of live forms passing through filters having a pore         size of between 100 and 20 nm     -   Direct detection of RNA-containing subunits of bacteria.

Different Primers have been Designed:

-   -   MOLL primers have been designed initially to detect mollicutes         (mycoplasma) species based on the conserved regions of the 16s         ribosomal RNA gene. In fact they can also detect gram positive         bacteria

1) Moll Outer Primer (sense) SEQ ID NO: 1 (AAYGGGTGAGTAACACGT), 2) Moll Outer Primer (antisense) SEQ ID NO: 2 (CCCGAGAACGTATTCACCG) 3) Moll Inner Primer (sense) SEQ ID NO: 3 (CTACGGGAGGCAGCAGTA) 4) Moll Inner Primer (antisense) SEQ ID NO: 4 (GTATCTAATCCTRTTTGCTCCCCA)

-   -   BACT primers will detect gram positive and gram negative         bacteria. The sequence of MOLL primers is included in the         degenerated sequence of the BACT primers.

1) Bact Outer Primer (antisense) SEQ ID NO: 5 (CCCGRGAACGTATTCACSG), 2) Bact Inner Primer (sense) SEQ ID NO: 6 (CTACGGGAGGCWGCAGTRRGGAAT), 3) Bact Inner Primer (antisense) SEQ ID NO: 7 (WGGGTATCTAATCCTRTTTGMTCCCCW)

-   -   The GNEG set of primers is specific of gram negative bacteria.         It differs from the Moll 16 out S by a single nucleotide

1) Gneg Outer Primer (sense) SEQ ID NO: 8 (RAYGGGTGAGTAAYGYMT),

The present invention therefore provides a method for identifying an RNA form of a bacteria, comprising reverse transcribing RNA material; conducting PCR using primers for a first highly conserved genetic sequence generic of the bacteria; conducting nested PCR using primers for a second highly conserved genetic sequence within the first amplified genetic sequence of the bacteria; and identifying the bacteria based on unconserved amplified sequences linked to the conserved sequences.

It is believed that the Nanoforms are a stable, low metabolic rate form of bacteria, which may be related to pathology, which have characteristic DNA which is generally undetectable by PCR or nested PCR. However, these organisms do have characteristic RNA, and therefore these can be detected by nested RT-PCR. Likewise, because these are now detectable according to the present invention, it is therefore possible to monitor and optimize treatments directed toward clearing these from infected subjects.

It is believed that Nanoforms are involved in human pathology, and further that these low metabolic organisms are involved in a constellation of chronic human diseases. Further, it is believed that some of these Nanoforms may be subcellular, that is, incomplete, and therefore may require association with other Nanoform, or other organisms or cells, for replication or reconstitution as a complete DNA bacterial form. Preliminary evidence suggests that the genetic material within a single Nanoforms is insufficient to reconstitute the entirety of a related bacterial (DNA) form, and therefore that multiple Nanoforms may be required in order to be self-replicating for the complete organism.

For example, multiple Nanoforms may infect a single cell, together constituting a complete genome for the associated DNA bacteria. Reverse transcriptase activity, for example, due to retroviruses, endogenous retroviral sequences, DNA pol I activity, etc., may be sufficiently active to generate the bacterial genome.

These Nanoforms may be biologically associated with retroviruses, such as HIV, which would therefore increase their likelihood of replication, since they would then carry their own reverse transcriptase, and potentially account for replication of sub-cellular fragments. The retroviruses may be passengers within the Nanoforms, and the Nanoforms represent an infectious particle for the virus.

The present invention reveals that the Nanoforms retain conserved sequences of 16S rRNA, and therefore may be targeted on this basis, for example by tetracycline analog antibiotics, especially administered over extended durations.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Material and Methods Oligonucleotide Primers.

The oligonucleotide primers used were:

1) Moll Outer Primer (sense) SEQ ID NO: 1 (AAYGGGTGAGTAACACGT), 2) Gneg Outer Primer (sense) SEQ ID NO: 8 (RAYGGGTGAGTAAYGYMT), 3) Bact Outer Primer (antisense) SEQ ID NO: 5 (CCCGRGAACGTATTCACSG), 4) Bact Inner Primer (sense) SEQ ID NO: 6 (CTACGGGAGGCWGCAGTRRGGAAT), and 5) Bact Inner Primer (antisense) SEQ ID NO: 7 (WGGGTATCTAATCCTRTTTGMTCCCCW)

-   -   where R=G or A, S=G or C, W=A or T, M=A or C, and Y=T or C.

Expected lengths of amplicons are ˜1,200 bp and ˜450 bp with the outer and inner primers, respectively. The primers employed were formulated as equal amounts of each primer within the class identified by the sequence.

Nucleic Acid Preparation and PCR/RT-PCR.

Cell line supernatants (400 μl), human plasma (200-400 μl) and human peripheral blood mononuclear cells (PBMC, 3-10 millions cells) were lyzed with 10 mMTris, pH7.4, 10 mM EDTA, 150 mM NaCl, 0.4% SDS, and 10 μg Proteinase K at 60° C. for 1 h. Nucleic samples were extracted three times with one volume of phenol/chloroform and one time with chloroform and precipitated by addition of 1/10 volume of 3M sodium acetate and two volumes of ethanol at −60° C. for 1 h. Samples were centrifuged 30 min. and the nucleic acid pellets were washed with 70% cold ethanol and solubilized in 10 mM Tris-HCI, pH 8.0. These preparations were stored at −60° C.

PCR reaction mix (50 μl) consisted of 5 mM MgCl2, 50 mM Tris, pH 8.0, 15 mM (NH4)2SO4, 10 mM B-Mercaptoethanol, 500 μM dATP, dCTP, dGTP, and DTTP, 0.025% BSA, 1 μM of each outer primer, 1 U Taq polymerase (Roche Molecular biochemicals, Laval, Canada), and 5-10 μl nucleic acid sample. For the first round PCR, the denaturation, annealing, and elongation temperatures and times used were 95° C. for 30 s, 42° C. for 30 s, and 78° C. for 2 m, respectively, for 42 cycles. After the final cycle, the products were kept at 78° C. for 10 m. One μl of the PCR product was subjected to a second round PCR with the set of inner primers. Denaturation, annealing, and elongation temperatures and times used were 95° C. for 30 s, 47° C. for 30 s, and 78° C. for 1 m, respectively, for 42 cycles, followed by a single incubation at 78° C. for 10 m. After the first and second round PCR, 10 μl of PCR product was analyzed by gel electrophoresis using 1.5% agarose, stained with ethidium bromide, visualized under ultraviolet light and photographed. Visible bands with appropriate size were cut and sequenced using the inner primers (DNA Landmarks, St-Jean sur le Richelieu, Canada). Sequence homology search was performed using the BLAST program of the NIH web site.

Samples negative for the appropriate band by PCR were subjected to a first round RT-PCR followed by a second round PCR. RT-PCR reaction mix (50 μl) consisted of 5 mM MgCl2, 50 mM Tris, pH 8.0, 15 mM (NH4)2SO4, 10 mM B-Mercaptoethanol, 500 μM dATP, dCTP, dGTP, and DTTP, 0.025% BSA, 1 μM of each outer primer, and Titan enzyme mix (Roche Molecular biochemicals, Laval, Canada), and 5 μl nucleic acid sample. The reverse transcription step was performed at 42° C. for 30 m. The first and second rounds PCR were performed as described above.

The precautions addressed elsewhere (Kwok and Higuchi, 1989) were followed to minimize the risk of false-positive results caused by the carry-over of previously amplified DNA. For example, extraction of nucleic acids and preparation of PCR/RT-PCR mix were performed under a sterile flow bench, only aliquoted reagents and filter tips were used, and negative controls were incorporated into each run.

Results All Samples:

First round PCR/RT-PCR: no detection of expected amplicon (˜1,200 bp).

Second round PCR (nested-PCR): all amplicon (˜450 bp) sequences related to bacterial 16S ribosomal RNA gene.

Patients' Lymphocytes (18 Samples):

No 450 bp amplicon detected by nested-PCR from first round PCR.

All samples positive (450 bp) by nested-PCR from RT-PCR.

Therefore, bacteria are in an “RNA state”, and are referred to herein as “Nanoforms”.

Samples of Patients' Plasma:

11 samples/12 positive for 450 bp amplicon by nested-PCR from first round PCR.

Discussion

Cell wall deficient pathogenic microorganisms, which may be mycoplasma, so-called L-forms, or potentially other types, are difficult to detect. Therefore, their involvement in pathology may be vastly under-reported.

It has been found, however, that these organisms have a well-conserved RNA sequences, such as the 16S rRNA, even when corresponding DNA or RNA is undetectable by a traditional polymerase chain reaction (PCR) or reverse transcriptase PCR (RT-PCR) method, which may be detected by nested RT-PCR amplification, using primers according to the present invention.

The present invention therefore provides a sensitive and specific method for detecting bacterial forms, which may be called “Nanoforms”, even when traditional methods fail. This therefore allows diagnosis of pathogens previously unrecognized, and monitoring of treatment thereof. 

1. A method for identifying an organism based on amplified genetic sequences, comprising the steps of: (1) reverse transcribing RNA to DNA within a sample with a viral reverse transcriptase; (2) initially conducting PCR using at least one outer primer having a sequence within the class: SEQ ID NO: 1 (AAYGGGTGAGTAACACGT) for Gram positive bacteria or, SEQ ID NO: 8 (RAYGGGTGAGTAAYGYMT) for Gram negative bacteria, and at least one primer having a sequence within the class: SEQ ID NO: 5 (CCCGRGAACGTATTCACSG), wherein R=G or A, S=G or C, W=A or T, M=A or C, and Y=T or C (3) subsequently conducting nested PCR, using inner primers, comprising at least one primer having a sequence within the class: SEQ ID NO: 6 (CTACGGGAGGCWGCAGTRRGGAAT), and at least one primer having a sequence within the class: SEQ ID NO: 7 (WGGGTATCTAATCCTRTTTGMTCCCCW); and (4) identifying the organism based on an amplified genetic sequence linked to the inner primers.
 2. The method according to claim 1, wherein the organism is unidentifiable by PCR or nested PCR if the sample is not subjected to reverse transcription.
 3. The method according to claim 1, wherein said PCR is conducted using all primers having sequences within SEQ ID NO: 1 or SEQ ID NO: 8, SEQ ID NO: 5, SEQ ID NO: 6 and SEQ ID NO:
 7. 4. The method according to claim 1, wherein said outer primer and inner primers comprise primers adapted to selectively amplify to a 16S ribosomal RNA sequence of the organism.
 5. A method for identifying an organism in a sample, the sample having inadequate DNA material characteristic of the organism to conduct the identification using PCR processes, comprising: (a) reverse transcribing RNA material within the sample to DNA using a Reverse Transcriptase (RNA-dependent DNA polymerase) enzyme; (b) conducting PCR using sense and antisense primers for a first highly conserved genetic sequence generic for the class of organism using a DNA Polymerase (DNA-dependent DNA polymerase) enzyme; (c) conducting nested PCR using sense and antisense primers for a second highly conserved genetic sequence, within the first highly conserved genetic sequence using a DNA Polymerase (DNA-dependent DNA polymerase) enzyme; and (d) identifying the organism based on an identification of at least one characteristic amplified sequence linked to at least one of the second highly conserved sequences.
 6. The method according to claim 5, wherein said first and second highly conserved genetic sequences each comprise a part of DNA sequence corresponding to a 16S ribosomal RNA sequence of the organism.
 7. The method according to claim 5, wherein at least one of the primers are part of a degenerate set, further comprising the step of employing a plurality of primers within the class definition of the degenerate set, wherein the degenerate set specifically targets variations within one of the first and second highly conserved sequences substantially without amplifying DNA unrelated to the first or second highly conserved sequences.
 8. The method according to claim 5, wherein PCR is conducted using primers comprising: at least one primer within the class: SEQ ID NO: 1 (AAYGGGTGAGTAACACGT) and SEQ ID NO: 8 (RAYGGGTGAGTAAYGYMT); and at least one primer having a sequence within the class: SEQ ID NO: 5 (CCCGRGAACGTATTCACSG), wherein R=G or A, S=G or C, W=A or T, M=A or C, and Y=T or C
 9. The method according to claim 5, wherein nested PCR is conducted using: at least one primer having a sequence within the class: SEQ ID NO: 6 (CTACGGGAGGCWGCAGTRRGGAAT), and at least one primer having a sequence within the class: SEQ ID NO: 7 (WGGGTATCTAATCCTRTTTGMTCCCCW), wherein R=G or A, S=G or C, W=A or T, M=A or C, and Y=T or C.
 10. The method according to claim 5, wherein said DNA Polymerase (DNA-dependent DNA polymerase) enzyme comprises a temperature resistant, DNA-dependent DNA Polymersase.
 11. The method according to claim 5, wherein: the PCR is conducted using all primer sequences falling within the class of at least one of: SEQ ID NO: 1 (AAYGGGTGAGTAACACGT) and SEQ ID NO: 8 (RAYGGGTGAGTAAYGYMT); and and all primer sequences falling within the class: SEQ ID NO: 5 (CCCGRGAACGTATTCACSG), wherein R=G or A, S=G or C, W=A or T, M=A or C, and Y=T or C.
 12. The method according to claim 5, wherein the nested PCR is conducted using: all primer sequences falling within the class: SEQ ID NO: 6 (CTACGGGAGGCWGCAGTRRGGAAT); and all primer sequences falling within the class: SEQ ID NO: 7 (WGGGTATCTAATCCTRTTTGMTCCCCW), wherein R=G or A, S=G or C, W=A or T, M=A or C, and Y=T or C.
 13. The method according to claim 5, wherein the organism is unidentifiable by PCR or nested PCR if the sample is not subjected to reverse transcription.
 14. The method according to claim 5, wherein said PCR step employs primers adapted to amplify a plurality of classes of organisms.
 15. A method for identifying an organism, comprising: (a) reverse transcribing RNA material in a sample to DNA with a reverse transcriptase (RNA-dependent DNA polymerase); (b) conducting PCR using sense and antisense primers for a first highly conserved 16S bacterial ribosomal sequence; (c) conducting nested PCR using sense and antisense primers for a second highly conserved 16S bacterial ribosomal sequence, within a PCR transcript derived from use of the PCR sense and antisense primers for amplifying the first highly conserved 16S bacterial ribosomal sequence; and (d) identifying the organism based on unconserved amplified 16S bacterial ribosomal sequences within a nested PCR transcript derived from use of the nested PCR sense and antisense primers for amplifying the second highly conserved 16S bacterial ribosomal sequence, wherein the organism is detectable even when organismal DNA in the sample is inadequate for PCR or nested PCR based identification.
 16. The method according to claim 15, wherein at least one of the primers are part of a degenerate set, further comprising the step of employing a plurality of primers within the specifications of the degenerate set.
 17. The method according to claim 15, wherein at least one of the primers are part of a degenerate set, further comprising the step of employing all primers within the specifications of the degenerate set. 